Strand-Specific RNA Sequencing for wild type and Drpd3 yeast entering quiescence [RNA-seq]
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE67149 | GEO | 2015/08/20
SECONDARY ACCESSION(S): PRJNA279128
REPOSITORIES: GEO
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Project description:Binding profiles for H3 and H4ac were determined as cells transition from log growth to quiescence. We found that massive chromatin changes that reflect global transcriptional repression occur after the diauxic shift in an Rpd3-dependent manner. Binding of Rpd3 is dramatically expanded to reflect binding at thousands of genes after quiescence entry, demonstrating an Rpd3-driven mechanism to change chromatin and repress transcription after entry into quiescence.
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Project description:Yeast (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.st (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
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